ramwasAnnotateLocations: Extract Biomart Annotation for a Vector of Locations.

In andreyshabalin/ramwas: Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

Description

Calls biomart annotation database for a vector of locations and assignes the tracks to the locations.

Usage

ramwasAnnotateLocations(param, chr, pos)

Arguments

param	List of parameters as described in the "RW6_param.Rmd" vignette. Try: vignette("RW6_param","ramwas").
chr	A vector of chromosome names or numbers.
pos	A vector of genomic locations on the chromosomes.

Details

This function is used internally by RaMWAS annotation step.

Value

An annotation table, on line per supplied location.

Author(s)

Andrey A Shabalin [e-mail]

See Also

See vignettes: browseVignettes("ramwas")

Examples

bihost = "grch37.ensembl.org"
bimart = "ENSEMBL_MART_ENSEMBL"
bidataset = "hsapiens_gene_ensembl"
biattributes = c("hgnc_symbol", "entrezgene", "strand")
bifilters = list(with_hgnc_trans_name = TRUE)
biflank = 0

param = ramwasParameters(
    bihost = bihost,
    bimart = bimart,
    bidataset = bidataset,
    biattributes = biattributes,
    bifilters = bifilters,
    biflank = biflank)

# Test a location
chr = "chr1"
pos =  15975530
## Not run: 
ramwasAnnotateLocations(param, chr, pos)

## End(Not run)

andreyshabalin/ramwas documentation built on Sept. 27, 2021, 7:25 p.m.